Went and worked at it some more and indeed, an adventurer can ride a cart from one fort to the other underground, passing between locations by jumping through fortifications carved into the border tiles. This requires going to the stone layers; fortunately i didn't have encompassing aquifers on the sites i went through.
The interesting thing is that you're not dependent on pre-existing passages (caverns or aboveground floor) and can thus isolate the cart track from the fort and any other outside influence. Chances are pretty good that some creature or other will still manage to spawn onto the track, so it's probably best to use a heavy cart, allowing you to just plow over them. Thanks to the magic of impulse ramps, all elevation changes are done on a single line of track, rideable in both directions. There's a track separation for the acceleration arrays, though.
If you make fort-mode test runs, better block off the ends of a fortification-connected track, or you'll end up with a cart stuck in a map-border fortification. Had to send my adventurer to get it back out, and jumping into a cart causes you to collide with it, which hurts. Fortunately, heal through fast travel still works, so i got use of my leg back.